[2024-01-24 15:26:55,155] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:55,162] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:55,162] [INFO] DQC Reference Directory: /var/lib/cwl/stg99167219-b233-4ce5-ad9c-7ba9b9242f13/dqc_reference
[2024-01-24 15:26:56,512] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,512] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,513] [INFO] Running command: gunzip -c /var/lib/cwl/stg77fb7661-8f7b-41f4-90fb-91220266fe6e/GCF_004328075.1_ASM432807v1_genomic.fna.gz | prodigal -d GCF_004328075.1_ASM432807v1_genomic.fna/cds.fna -a GCF_004328075.1_ASM432807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:10,252] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:10,252] [INFO] Task started: HMMsearch
[2024-01-24 15:27:10,252] [INFO] Running command: hmmsearch --tblout GCF_004328075.1_ASM432807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99167219-b233-4ce5-ad9c-7ba9b9242f13/dqc_reference/reference_markers.hmm GCF_004328075.1_ASM432807v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:10,555] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:10,556] [INFO] Found 6/6 markers.
[2024-01-24 15:27:10,596] [INFO] Query marker FASTA was written to GCF_004328075.1_ASM432807v1_genomic.fna/markers.fasta
[2024-01-24 15:27:10,597] [INFO] Task started: Blastn
[2024-01-24 15:27:10,597] [INFO] Running command: blastn -query GCF_004328075.1_ASM432807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99167219-b233-4ce5-ad9c-7ba9b9242f13/dqc_reference/reference_markers.fasta -out GCF_004328075.1_ASM432807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:11,691] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:11,694] [INFO] Selected 28 target genomes.
[2024-01-24 15:27:11,695] [INFO] Target genome list was writen to GCF_004328075.1_ASM432807v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:11,710] [INFO] Task started: fastANI
[2024-01-24 15:27:11,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg77fb7661-8f7b-41f4-90fb-91220266fe6e/GCF_004328075.1_ASM432807v1_genomic.fna.gz --refList GCF_004328075.1_ASM432807v1_genomic.fna/target_genomes.txt --output GCF_004328075.1_ASM432807v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:40,742] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:40,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99167219-b233-4ce5-ad9c-7ba9b9242f13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:40,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99167219-b233-4ce5-ad9c-7ba9b9242f13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:40,764] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:40,765] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:40,765] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	78.642	555	1626	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	78.3017	505	1626	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	78.285	687	1626	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	78.1497	448	1626	95	below_threshold
Chthonobacter albigriseus	strain=KCTC 42450	GCA_013839445.1	1683161	1683161	type	True	78.0431	432	1626	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	78.011	478	1626	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.8017	459	1626	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	77.7952	452	1626	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	77.7881	456	1626	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	77.7194	399	1626	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	77.5486	495	1626	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	77.517	449	1626	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.4854	444	1626	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.4239	476	1626	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	77.397	534	1626	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.3901	493	1626	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.3378	490	1626	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	77.3359	391	1626	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	77.3072	295	1626	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.1928	564	1626	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	77.1855	340	1626	95	below_threshold
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	77.1574	274	1626	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	77.1529	559	1626	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.1112	629	1626	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.0306	611	1626	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	77.013	444	1626	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	76.9729	417	1626	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	76.8287	451	1626	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:40,767] [INFO] DFAST Taxonomy check result was written to GCF_004328075.1_ASM432807v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:40,767] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:40,767] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:40,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99167219-b233-4ce5-ad9c-7ba9b9242f13/dqc_reference/checkm_data
[2024-01-24 15:27:40,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:40,818] [INFO] Task started: CheckM
[2024-01-24 15:27:40,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004328075.1_ASM432807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004328075.1_ASM432807v1_genomic.fna/checkm_input GCF_004328075.1_ASM432807v1_genomic.fna/checkm_result
[2024-01-24 15:28:47,980] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:47,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:47,998] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:47,999] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:47,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004328075.1_ASM432807v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:47,999] [INFO] Task started: Blastn
[2024-01-24 15:28:47,999] [INFO] Running command: blastn -query GCF_004328075.1_ASM432807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99167219-b233-4ce5-ad9c-7ba9b9242f13/dqc_reference/reference_markers_gtdb.fasta -out GCF_004328075.1_ASM432807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:50,155] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:50,158] [INFO] Selected 7 target genomes.
[2024-01-24 15:28:50,158] [INFO] Target genome list was writen to GCF_004328075.1_ASM432807v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:50,163] [INFO] Task started: fastANI
[2024-01-24 15:28:50,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg77fb7661-8f7b-41f4-90fb-91220266fe6e/GCF_004328075.1_ASM432807v1_genomic.fna.gz --refList GCF_004328075.1_ASM432807v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004328075.1_ASM432807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:59,153] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:59,160] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:59,161] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_004328075.1	s__Siculibacillus lacustris	100.0	1623	1626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Siculibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_019160155.1	s__Pinisolibacter aquiterrae	82.2559	899	1626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	96.46	96.46	0.88	0.88	2	-
GCA_002298965.1	s__Pinisolibacter sp002298965	82.1428	694	1626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517025.1	s__Pinisolibacter sp012517025	82.0512	703	1626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305515.1	s__Prosthecomicrobium_A hirschii	79.1011	711	1626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	97.89	97.89	0.95	0.95	2	-
GCA_018729455.1	s__Prosthecomicrobium_A sp018729455	78.8898	711	1626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192745.1	s__Polymorphum gilvum	77.9342	477	1626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:59,162] [INFO] GTDB search result was written to GCF_004328075.1_ASM432807v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:59,163] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:59,167] [INFO] DFAST_QC result json was written to GCF_004328075.1_ASM432807v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:59,167] [INFO] DFAST_QC completed!
[2024-01-24 15:28:59,167] [INFO] Total running time: 0h2m4s